WOMBATS!

Recently I was having a stressful, intense time a work. Deadlines forced me to work very long hours in front of a computer and eat poorly, things that wreak havoc on one's mental health. I needed a cure, something that could restore mental balance and relieve my stress instantly, with little or no side effects. According to Science-Based Medicine, no such cure exists, so I was forced to turn to "traditional" or "alternative" methods. And what is the most effective alternative medicine to restore mental balance and eliminate stress? WOMBATS.

Nothing cures stress like this adorable face.

After I finally completed my work, I needed some wombat cuddles and thankfully there's a wombat rehabilitation sanctuary not far from Canberra. The Sleepy Burrows Wombat Sanctuary is located on farmland about an hour outside of Canberra and it is chock full of wombats. Sleepy Burrows is run by  a woman named Donna, with the help of her husband Phil, out of their home. The youngest wombats need the most attention, and these are cared for in the house. This results in some pretty adorable, and undeniably Australian, domestic scenes:

Donna and Phil rescue wombats from the Southern Highlands area, and judging by the number of wombats they have, there are a lot of wombats in the area that need rescuing! Wombats come to Donna generally because they were injured by a car, they were orphaned by a car, or because someone thought that a wombat would make a nice pet. People who bring a wombat home as a pet invariably end up giving them to someone like Donna who (1) knows what they're doing and (2) has a large, rural property because WOMBATS MAKE TERRIBLE PETS.

Wombats are cute, and I can see why someone might decide that a baby wombat would be nice to keep as a pet. Nonetheless, I cannot stress this enough: WOMBATS ARE NOT PETS. Trying to keep a wombat as a pet is like trying to keep a sentient bulldozer as a pet. Wombats are large, wild animals and they need large, wild places to live. They like to dig, and if they're living on carpet, vinyl or hardwood, that's what they'll dig.

Another reason wombats make terrible pets is that they think it's hilarious to nip. When Donna brought out the young wombats to meet us on her living room floor, her two (human) children immediately pulled their legs up onto the couch. They already knew what we were about to learn: wombats are nippy! They give us what they must think are small nips, but their teeth are built for the same purpose as a lawn mower, and a small nip from a wombat is about as pleasant as what I would imaging a small nip from a lawnmower would feel like.

Dawn fortunately preferred to nip my shoe. I was not so lucky with all the wombats.

Other than unwanted pets, the primary source of wombats for the Sleepy Burrows Sanctuary is roadside mortality. Donna gets a lot of wombats that have been hit by cars. Most, unfortunately, are unable to survive and have to be euthanised. Some lucky ones Donna nurses back to health. More often, though, the adult wombat dies and leaves behind an orphaned baby wombat. Unfortunately, dead wombats by the side of the road are a familiar sight to anyone who drives around the Southern Highlands of Australia. As well as cars, there are introduced diseases that debilitate the wombats mentally and send them wandering aimlessly, unable to function. Dawn (pictured above) had such a disease and though she recovered, she's forever mentally debilitated and is living out her days at the sanctuary.

What was really shocking to me was that apparently there are people who like to use wombats as target practice. Wombats are big, tough animals with thick skin, and only high caliber bullets kill them quickly. Donna often gets called to wombats that seem injured or disoriented, only to find a small hole from a small caliber bullet somewhere in the poor thing's hide, slowly killing it. These wombats often have to be put down, and those that don't cost a lot of money in vet bills to recover. And target practice wasn't the whole picture of cruelty. The stories I heard of the horrible things people do to wombats for entertainment was sickening.

That people are willing to do such terrible things to wombats just makes Sleepy Burrows all the more necessary. Donna not only takes in the sick, injured, orphaned and/or tortured wombats, she also talks to people in the community, especially people in rural communities who encounter wombats on a regular basis, to try and foster more of a sense of compassion towards the animals. Sharing the love of animals is just about the only way to protect them for the long term, and it's people like Donna who are doing that work.

Of course the primary goal of any wildlife sanctuary should be returning animals to the wild. Sleepy Burrows has an amazing track record of releasing wombats when they are ready and able to survive. Donna is fortunate to live on a large, wild property suitable for wild wombats, and also to have supportive neighbours who appreciate wombats on their properties. When the wombats are ready, they're released into suitable habitat and Donna has great evidence that they are surviving and thriving. It helps that she can somehow recognise all the wombats as individuals! To train up and "educate" the wombats, Donna has set up what she calls "Wombat University", a series of enclosures where the wombats go from "extremely coddled" to "almost wild". She moves each wombat through the levels at their own pace. Wombats, like people, have personalities, and different individuals learn at different speeds. At Wombat University (unlike at Human University, I'd like to point out) each wombat learns at their own speed, and is only sent to the next level when they're ready.

Donna runs her sanctuary very efficiently, and she has to! Other than her husband Phil, who helps as much as he can but also works full time, it's just her by herself rescuing, caring for, and rehabilitating a heck of a lot of wombats. What she does isn't cheap, either. Donna welcomes visitors (which is extra generous because there's no public facility, visitors are welcomed into her home) for a donation, as I made when I visited. She also has an online store selling some awesome wombat stuff, and a coffee club for Wombassators who would like to support Sleepy Burrows monthly. Sleepy Burrows is an amazing place and the only place that I know of that you can cuddle baby wombats for hours on end (I think we were there for about four hours, and in the end we left only because we were exhausted from all the wombat cuddling!) They definitely deserve support for all their amazing efforts.

What bird is this?

At the beginning of February, on a camping trip to Wilson's Promontory National Park, I saw a fledgling bird and to this day I have no idea what kind of bird it is. I like birds, and I like to watch them, so while I'm not an expert bird-identifier, I'm no slouch in the department either. However, this young bird has me completely stumped. If you know what kind of bird this is, please let me know!

Update: It's a juvenile eastern yellow-robin. Thanks, everyone!

Happy International Women's Day!

Today is International Women's Day, an awareness-raising day the world needs because many facets of society do not recognise women as equals, including (1) men and (2) Hollywood. So I thought, as a member of the former, I would share some recent experiences I've had with the latter, and in doing so try to do my own small part to promote gender equality.

The Bechdel Test is an excellent metric for women's representation in film. It's an extremely basic test, requiring only that there be two named female characters in a film who talk to each other about something other than a man. Despite the test's simplicity, a shockingly high number of movies fail the test. For example, of this year's best picture nominees, only two out of eight pass the Bechdel. It's been said time and time again that the test shouldn't be used to condemn any one particular movie, but rather as a critique of Hollywood as a whole. That this or that particular movie doesn't pass the Bechdel is no big deal, the problem is that the film industry is consistently churning out movies that underrepresent, exploit, and ignore women. 

One reason that movies often fail the Bechdel is that they generally have one main character, and therefore the supporting characters generally spend their time talking to, and about, the main character. As long as main characters continue to be mostly male, movies will continue to fail the Bechdel. The last three movies I've seen in theatre are Birdman (this year's Oscar winner), Still Alice, and Respire (Breathe). These three movies are all character studies and as such revolve strongly around their respective main characters.

Birdman's main character is a man, and it fails the Bechdel test in my opinion. The problem here is that the Bechdel test is vulnerable to technicalities. Some argue that Birdman passed based on an extremely short part of a longer conversation (about men) where two women briefly digress to talking about not-men. And then the two women kiss for no reason.

Still Alice and Respire, on the other hand, both feature women as their main characters and both pass the Bechdel with flying colours. Female characters in both these films have many varied conversations that have nothing to do with men. There is a huge difference between these movies and what some argue constitutes passing the Bechdel in the case of Birdman. There's also the added positive of no random, inexplicable female-female make-out sessions in these movies. What I'd like to point out is that both movies fail the reverse Bechdel, which means applying the metric to men instead of women (Birdman passes the reverse Bechdel). According to IMBD, very very few movies fail the reverse Bechdel.  

We should applaud movies that pass the Bechdel. To me that means we should applaud movies that have both men and women in important roles that don't exist primarily as love-interests or other gender stereotypes. However, if we recognise that a lot of movies are heavily main-character-focussed and that these movies are only likely to pass with women in the main role, maybe we should start keeping track of which movies pass the reverse Bechdel as well. Maybe, in addition to increasing the number of movies that pass the Bechdel test, we should get the number of movies failing the Bechdel to an equal number as those that fail the reverse Bechdel.

The basics of using the Pool to open and view images and label fields

I've spent a good portion of my PhD working with 3D images in the program Avizo, which is essentially the same as the program Amira. This involved a steep learning curve and a lot of problem solving in the beginning. I've decided to write about the problems I've encountered and how I dealt with them in the hope that this may help the next person learning to use Avizo or Amira do so a bit faster, and with less frustration along the way. These problems will look trivial to the regular or advanced Amira/Avizo user, but they were quite frustrating at the time! These posts assume the reader's familiar with sections 2.1-2.5 of the Amira user's guide, which cover how to load, view and segment an image. My introductory post on this topic is here.

Figuring out how the basics of how the "Pool" (in Amira) or the "Project View" (in Avizo) works can be a bit tricky, and it's one of the first things you have to figure out to use these programs. The Pool is where all the data and modules you're working with are visualised. Here's how the Amira User Manual describes the Pool and its contents:

"Amira is a modular and object-oriented software system. Its basic system components are modules and data objects. Modules are used to visualize data objects or to perform some computational operations on them. The components are represented by little icons in the Pool. Icons are connected by lines indicating processing dependencies between the components, i.e., which modules are to be applied to which data objects." - Amira User Manual, page 4

This is basic stuff, but if you're new to Amira/Avizo, confusion arises because nowhere does the manual tell you what any of this stuff looks like. Here's what it looks like in Avizo, and it looks pretty much the same as this in Amira:

Screen Shot 2015-01-07 at 3.08.25 pm.png

So data objects and modules are colourful blobs, connections between data objects and modules are blue lines, and if you look closely, you can see that the data object-end of the blue line is a diamond while the module-end of the blue line is a square. 

The Amira User Manual explains very well how to make a new label field for an image, and how to save the whole thing (image + label field) together as a "project". But what if you have an image and a label field already, and would like to join them? The Amira User Manual, as far as I can tell, doesn't cover this. Here's how to connect two data objects, one of which is a 3D image and the other is a label field. First, open the 3D image:

Then, open the label field:

The data object for the label field appears below the data object for the 3D image, unconnected. Now, click on the white square of the label field's data object, which allows you to control what it's connected to. It gives you a drop-down list of different kinds of connections it can make, select the "ImageData" option. A blue connection line follows your cursor around, click on the 3D image's data object. The two data objects jump together, indicating that they are now connected. Notice that connections between data objects are displayed differently than connections between a data object and a module.

All this is well and good, but if you've done this, you've noticed that none of this results in you actually visualising anything. Fortunately, the Amira User Manual is very good at explaining how to visualise your data, in general. However, one thing that I think is missing from the manual is how to visualise a label field and the image it's based on at the same time. For this, there's Colorwash, section 2.8.3 in the Amira User Manual. Colorwash is described in the manual as being for the visualisation of two images at once, but it's not clear from their description that it can be used to visualise a label field on top of an image. Technically a label field is just an image dataset like any other, so Colorwash can be used like this. Attach a OrthoSlice module to the 3D image data object, then attach a Colourwash module to the OrthoSlice module. Click on the white box in the Colourwash module, select "Data" from the drop-down list, and click on the label field data object. Notice that connections between modules are displayed the same way as connections between data objects.

There! Quick and easy ways to load and visualise images and their label fields.

Here are some photos of a very cool lizard

One of Australia's most famous and charismatic animals is the thorny devil (Moloch horridus). It's famous because it looks cool, and because it's not all that easy to find. It's also the only member of the amphibolurine agamids that isn't referred to as a dragon. Although... dragon... devil... I can see a theme here. 

I found my first thorny devil in 2005, when I was an 18-year-old backpacking around Australia. It was crouched down on the Barkly Highway as we were driving between Camooweal and the Northern Territory border. My travel companion - the owner and driver of the car - was getting annoyed at me because I kept yelling for him to stop for animals, and by the time we stopped the animal would be gone (this is a frequent problem when driving at 110 km/hr). I promised him that this time the animal would still be there, and thankfully he stopped. I was so overjoyed I even went to the trouble of taking a picture of it. Here it is:

I am not a photographer. There are better pictures coming.

Not that you can tell from that picture, but the thorny devil is a really weird, unique, beautiful lizard.  Better views of thorny devils can be had by looking at Angus Kennedy's pictures from my 2012 field season. While Angus and Mitch were helping me catch dragons in the Northern Territory and South Australia we came across three thorny devils.

This is the standard thorny devil pose that appears in pretty much all books about Australian reptiles and wildlife. Thurlga Station, South Australia, 2012. Photo by Angus Kennedy.

The thorny devil lives in Australia's more foreboding habitat, the dry, arid interior, where water is a valuable commodity. Its scales are specially designed so that, when any part of the lizard comes in contact with water, that water is funnelled to its mouth through capillary action, the same process that gets water from the roots to the leaves of trees. This was such an incredible discovery that its original description was published in Nature, one of the most important scientific journals. Subsequently, it has been a continuing area of interest for biologists.

A thorny devil at the entrance to an ant's nest. Thurlga Station, South Australia, 2012. Photo by Angus Kennedy.

Other than the water-funnelling thing, there's not much known about thorny devils. A Google Scholar search for their scientific name turns up only thirty two results, many of which are observations of their basic natural history. They're famous for eating ants, and this paper has an adorable picture of one in "characteristic feeding posture" eating ants off the side of a tree. That so little is know about such a famous and charismatic animal is alarming; I can't even find population estimates for them.

Unlike most dragons, the thorny devil ambles slowly. Thurlga Station, South Australia, 2012. Photo by Angus Kennedy.

An additional theme I can see in the limited literature is that thorny devils are slow. In fact, in one of the most hilarious titles to a scientific paper I've ever seen, this article asks "is the devil a sloth?" Although we all know what the authors mean, and scientists are not without a sense of humour (well, most of us, anyway), sloths are, in fact, animals (mammals of the order Pilosa) and thorny devils are definitely not sloths.

Thorny devils have a weird protuberance coming out of the back of their neck. Thurlga Station, South Australia, 2012. Photo by Angus Kennedy.

There's a weird lump coming out the back of the thorny devil's neck. I've heard it said that this is a false head, and that if a thorny devil feels threatened it'll crouch down and stick up its false head for sacrifice to the predator. I can't find any evidence for this in the literature. It is true that, when threatened, the thorny devil will crouch down and arch it back, but this is standard posture for animals that have spiky backs: it presents the predator with their least palatable body part. This behaviour can be seen spike-backed creatures like porcupines, hedgehogs, echidnas, lion fish, armadillo lizards and those horrible spiky caterpillars that curl up in a ball when you touch them. Furthermore, at an extremely informal poll at last year's meeting of Australian herpetologists, I couldn't find anyone who's ever seen a thorny devil without that weird lump. Geckos and skinks, which wiggle their tails to fool predators, are frequently found without tails, and have even evolved a mechanism for automatically detaching their tails and growing new ones. Not that I'm saying the false-head explanation isn't true, but just that I haven't heard of any convincing evidence. If you know of any evidence for the use of the weird lump, I'd be curious to hear it.

Thorny devils are spectacularly coloured and patterned. Thurlga Station, South Australia, 2012. Photo by Angus Kennedy.

Thorny devils are a good example of disruptive colouration. Their colours are the same colours as arid Australia, and they are patterned in such a way that it's hard to make out the shape of the lizard, especially if it's against a complex background. Of course, in these pictures, where we've deliberately placed the lizard against the homogenous backdrop of a dirt road, and it's easy to see.

Thorny devils are the opposite of dolphins: they always look grumpy. Thurlga Station, South Australia, 2012. Photo by Angus Kennedy.

One paper, that I admit is not the most convincing, suggests another adaptation that thorny devils have to their arid home: they may pee on their eggs to keep the eggs moist.

Such a cool lizard! Thurlga Station, South Australia, 2012. Photo by Angus Kennedy.

I thought I'd end with a picture I found online. Thorny devils are quite dramatic looking, especially head-on, but I've never seen them look quite as terrifying as in this artificially-coloured image of a thorny devil skull overlayed onto an image of its head, taken from this website.

The thorny devil at its most terrifying, courtesy of digimorph.org.

The thorny devil at its most terrifying, courtesy of digimorph.org.